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MPQC
3.0.0-alpha
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This is the complete list of members for sc::MolecularFragment, including all inherited members.
| add_atom(int Z, double x, double y, double z, const std::string &label="", double mass=0.0, int have_charge=0, double charge=0.0, int have_fragment=0, int fragment=0) | sc::Molecule | |
| any_atom_has_charge() const | sc::Molecule | |
| any_atom_has_fragment() const | sc::Molecule | |
| any_atom_has_label() const | sc::Molecule | |
| atom(size_t i) const (defined in sc::Molecule) | sc::Molecule | inline |
| atom_at_position(double *, double tol=0.05) const | sc::Molecule | |
| atom_label_to_index(const std::string &label) const | sc::Molecule | |
| atom_name(int iatom) const | sc::Molecule | |
| atom_symbol(int iatom) const | sc::Molecule | |
| atom_to_uniq_ (defined in sc::Molecule) | sc::Molecule | protected |
| atom_to_unique(int iatom) const | sc::Molecule | inline |
| atom_to_unique_offset(int iatom) const | sc::Molecule | |
| atominfo() const | sc::Molecule | inline |
| atominfo_ (defined in sc::Molecule) | sc::Molecule | protected |
| atoms() const (defined in sc::Molecule) | sc::Molecule | inline |
| atoms_ (defined in sc::Molecule) | sc::Molecule | protected |
| center_of_mass() const | sc::Molecule | |
| charge(int iatom) const | sc::Molecule | |
| charges() const | sc::Molecule | |
| class_desc() const MPQC__NOEXCEPT | sc::DescribedClass | |
| class_name() const | sc::DescribedClass | |
| class_version() const | sc::DescribedClass | |
| cleanup_molecule(double tol=0.1) | sc::Molecule | |
| clear() (defined in sc::Molecule) | sc::Molecule | protected |
| clear_symmetry_info() (defined in sc::Molecule) | sc::Molecule | protected |
| dereference() | sc::RefCount | inline |
| DescribedClass() (defined in sc::DescribedClass) | sc::DescribedClass | |
| DescribedClass(const DescribedClass &) (defined in sc::DescribedClass) | sc::DescribedClass | |
| dir_restore_state(StateIn &si, const char *objectname, const char *keyword=0) (defined in sc::SavableState) | sc::SavableState | static |
| equiv_ (defined in sc::Molecule) | sc::Molecule | protected |
| equivalent(int iuniq, int j) const | sc::Molecule | inline |
| fragment(int atom) const | sc::Molecule | |
| geometry_units() const | sc::Molecule | inline |
| geometry_units_ (defined in sc::Molecule) | sc::Molecule | protected |
| has_inversion(SCVector3 &origin, double tol=1.0e-8) const | sc::Molecule | |
| highest_point_group(double tol=1.0e-8) const | sc::Molecule | |
| identifier() const | sc::RefCount | inline |
| include_q() const | sc::Molecule | inline |
| include_q_ (defined in sc::Molecule) | sc::Molecule | protected |
| include_qq() const | sc::Molecule | inline |
| include_qq_ (defined in sc::Molecule) | sc::Molecule | protected |
| init_symmetry_info(double tol=0.5) (defined in sc::Molecule) | sc::Molecule | protected |
| is_axis(SCVector3 &origin, SCVector3 &udirection, int order, double tol=1.0e-8) const | sc::Molecule | |
| is_linear(double tolerance=1.0e-5) const | sc::Molecule | |
| is_linear_planar(int &linear, int &planar, double tol=1.0e-5) const | sc::Molecule | |
| is_planar(double tolerance=1.0e-5) const | sc::Molecule | |
| is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const | sc::Molecule | |
| is_Q(int iatom) const | sc::Molecule | |
| key_restore_state(StateIn &si, const char *keyword) | sc::SavableState | static |
| label(int atom) const | sc::Molecule | |
| lock_ptr() const | sc::RefCount | |
| managed() const (defined in sc::RefCount) | sc::RefCount | inline |
| mass(int atom) const (defined in sc::Molecule) | sc::Molecule | |
| max_z() | sc::Molecule | |
| MolecularFragment(const Ref< KeyVal > &kv) | sc::MolecularFragment | |
| MolecularFragment(StateIn &) (defined in sc::MolecularFragment) | sc::MolecularFragment | |
| Molecule() (defined in sc::Molecule) | sc::Molecule | |
| Molecule(const Molecule &) (defined in sc::Molecule) | sc::Molecule | |
| Molecule(StateIn &) (defined in sc::Molecule) | sc::Molecule | |
| Molecule(const Ref< KeyVal > &input) | sc::Molecule | |
| move_to_com() (defined in sc::Molecule) | sc::Molecule | |
| n_core_electrons() | sc::Molecule | |
| n_non_q_atom() const | sc::Molecule | inline |
| n_q_atom() const | sc::Molecule | inline |
| natom() const | sc::Molecule | inline |
| nequiv_ (defined in sc::Molecule) | sc::Molecule | protected |
| nequivalent(int iuniq) const | sc::Molecule | inline |
| non_q_atom(int i) const | sc::Molecule | inline |
| non_q_atoms_ (defined in sc::Molecule) | sc::Molecule | protected |
| nreference() const | sc::RefCount | inline |
| nuclear_charge_efield(const double *charges, const double *position, double *efield) | sc::Molecule | |
| nuclear_efield(const double *position, double *efield) | sc::Molecule | |
| nuclear_repulsion_1der(int center, double xyz[3]) | sc::Molecule | |
| nuclear_repulsion_energy() | sc::Molecule | |
| nuniq_ (defined in sc::Molecule) | sc::Molecule | protected |
| nunique() const | sc::Molecule | inline |
| operator=(const Molecule &) (defined in sc::Molecule) | sc::Molecule | |
| operator=(const SavableState &) (defined in sc::SavableState) | sc::SavableState | |
| operator=(const DescribedClass &) (defined in sc::DescribedClass) | sc::DescribedClass | |
| operator=(const RefCount &) (defined in sc::RefCount) | sc::RefCount | inlineprotected |
| pg_ (defined in sc::Molecule) | sc::Molecule | protected |
| point_group() const | sc::Molecule | |
| principal_moments_of_inertia(double *evals, double **evecs=0) const | sc::Molecule | |
| print(std::ostream &=ExEnv::out0()) const | sc::Molecule | virtual |
| print_parsedkeyval(std::ostream &=ExEnv::out0(), int print_pg=1, int print_unit=1, int number_atoms=1) const (defined in sc::Molecule) | sc::Molecule | virtual |
| print_xyz(std::ostream &=ExEnv::out0(), const char *title=0) const (defined in sc::Molecule) | sc::Molecule | |
| q_atom(int i) const | sc::Molecule | inline |
| q_atoms_ (defined in sc::Molecule) | sc::Molecule | protected |
| q_Z_ (defined in sc::Molecule) | sc::Molecule | protected |
| r(int atom, int xyz) (defined in sc::Molecule) | sc::Molecule | inline |
| r(int atom, int xyz) const (defined in sc::Molecule) | sc::Molecule | inline |
| r(int atom) const (defined in sc::Molecule) | sc::Molecule | inline |
| ref() | sc::DescribedClass | inline |
| ref_origin() const | sc::Molecule | inline |
| ref_origin_ (defined in sc::Molecule) | sc::Molecule | protected |
| RefCount() (defined in sc::RefCount) | sc::RefCount | inlineprotected |
| RefCount(const RefCount &) (defined in sc::RefCount) | sc::RefCount | inlineprotected |
| reference() | sc::RefCount | inline |
| restore_state(StateIn &si) | sc::SavableState | static |
| SavableState() (defined in sc::SavableState) | sc::SavableState | protected |
| SavableState(const SavableState &) (defined in sc::SavableState) | sc::SavableState | protected |
| SavableState(StateIn &) | sc::SavableState | protected |
| save_data_state(StateOut &) | sc::MolecularFragment | virtual |
| save_object_state(StateOut &) | sc::SavableState | |
| save_state(StateOut &) | sc::SavableState | |
| save_state(SavableState *s, StateOut &) (defined in sc::SavableState) | sc::SavableState | static |
| save_vbase_state(StateOut &) | sc::SavableState | virtual |
| set_include_q(bool iq) | sc::Molecule | inline |
| set_include_qq(bool iqq) | sc::Molecule | inline |
| set_point_group(const Ref< PointGroup > &, double tol=1.0e-7) | sc::Molecule | |
| symmetrize(double tol=0.5) | sc::Molecule | |
| symmetrize(const Ref< PointGroup > &pg, double tol=0.5) | sc::Molecule | |
| throw_if_atom_duplicated(int begin=0, double tol=1e-3) (defined in sc::Molecule) | sc::Molecule | protected |
| total_charge() const | sc::Molecule | |
| total_Z() const | sc::Molecule | |
| transform_to_principal_axes(int trans_frame=1) (defined in sc::Molecule) | sc::Molecule | |
| transform_to_symmetry_frame() (defined in sc::Molecule) | sc::Molecule | |
| translate(const double *r) (defined in sc::Molecule) | sc::Molecule | |
| unique(int iuniq) const | sc::Molecule | inline |
| unlock_ptr() const | sc::RefCount | |
| unmanage() | sc::RefCount | inline |
| use_locks(bool inVal) | sc::RefCount | |
| Z(int atom) const (defined in sc::Molecule) | sc::Molecule | inline |
| ~DescribedClass() (defined in sc::DescribedClass) | sc::DescribedClass | virtual |
| ~MolecularFragment() (defined in sc::MolecularFragment) | sc::MolecularFragment | virtual |
| ~Molecule() (defined in sc::Molecule) | sc::Molecule | virtual |
| ~RefCount() (defined in sc::RefCount) | sc::RefCount | virtual |
| ~SavableState() (defined in sc::SavableState) | sc::SavableState | virtual |